The Booth on the Brain
by I'dRatherBeInStarsHollow
Summary: Brennan boards her flight to Jakarta with a little more than human remains on her mind. Set after the Season 5 finale, 'The Beginning in the End'.
1. Chapter 1

**Brennan boards her flight to Jakarta with a little more than human remains on her mind. Set after the Season 5 finale, 'The Beginning in the End'.**

 **A/N: So... This is my first Bones fic and it all came out in a bit of a rush so I hope it's okay. I found the eps after the 100th really interesting because neither of Brennan nor Booth could _really_ go back to normal, no matter how hard Brennan tried... This is just my thoughts on Brennan's thoughts after their parting - I reckon she's savvier than she lets on but just thinks she's doing the better thing.**

 **Also, if I were Hart Hanson, I'd have some canon _Bones_ to write so... Not me.**

The Booth on the Brain

Brennan stowed her bag carefully in the overhead compartment and sat down in her seat. She didn't think she'd ever been more grateful for the fact that she didn't have to fly coach - as intelligent as Daisy was, incessant chatter wasn't what Brennan needed right now. Right now, she needed some time alone with her thoughts.

She breathed out heavily and felt her eyes well up. It was okay when she was moving, busy, purposeful but whenever she paused to think about anything - which always ended up with her thinking about everything - she found she struggled to contain her emotions. And so she started with the things she knew, in an attempt to gain some semblance of control.

She knew that she wanted to be going to the Maluku Islands. For anthropology. For herself.

She knew that she needed time away from D.C.

She knew that, despite that, a part of her was still back in the Royal Diner, waiting for her partner, for Booth. For Booth, who had snuck of base to say goodbye:

She knew she was glad she'd gotten to see Booth again.

It had been a shock to see him in his uniform. Sure, she'd seen pictures before but they were of a younger Booth, Booth the boy, not the Booth she knew now. It scared her, the uniform. Brought home to her where he was going - that she couldn't follow him there. Another deep breath.

She knew she had to have some time apart from Booth.

She knew things couldn't keep going like they had been, that something had had to give. Because she had told him no, because she couldn't gamble, couldn't change. She had told him no. Brennan stood by her decision; she wasn't what Booth needed in a relationship. They weren't a logical match. And yet, with her eyes closed, she could still see his face outside Sweets' office building. Could hear herself pleading with him to continue their partnership in spite of it all…

What were they doing now then? Voluntarily running from each other, even when it felt… Booth would probably say it felt like losing a limb and although, scientifically, that was incorrect, Brennan felt the metaphor might have some credence after all. When she'd let go of his hand in the terminal, it had felt a lot like losing an extension of herself.

She shook her head. There was no real reason to be sad; a year from now, she would see Booth again - and Angela and Hodgins and Cam, even Sweets. They would all still be friends. Somehow, though, things felt a lot like they were ending.

Brennan saw Booth's face behind her eyelids, turning back to look at her. One year.


	2. Chapter 2

**A/N: Inspired by Brennan's confessions in S6E2 about the extent to which she thought about Booth in the Maluku islands. Quite a different tone to the last chapter so let me know your thoughts if you feel like it...**

 **Still not Hart Hanson.**

Chapter 2

Brennan went four days without thinking about DC. On the fifth morning, she woke up from a vivid dream about being on a case with Booth and found that she was disappointed that it wasn't her reality. And that wasn't what she had expected at all. As such, she gave herself permission, from then on, to think about DC, and about Booth, as much as she wanted; that way, she hoped, she would be able to assess what she was really feeling and why (Booth did always stress the importance of motive). Besides, it couldn't hurt here in the wilderness, about as far away from Brennan's normal life as she could get (which was, of course, precisely the point).

From then on, in a lot of ways, she didn't really feel apart from Booth anymore because he was in her every thought, informing her every decision. When she drove, Brennan thought about how Booth driving her around in the SUV. When _Daisy_ drove, Brennan appreciated Booth's stable driving more than ever. He was with her when she least expected it, making her laugh at the smallest, everyday things just because they reminded her of him. She didn't normally get the opportunity to really think about their partnership and what it meant; after this, she thought she might do it more often. But it _was_ special here, in the Maluku islands, because she could think unhindered. There were only things to trigger positive memories and none to remind her of the difficulties they faced. Everything was out of context here - and to Brennan, that was the only way she and Booth could ever really work.

Here, she could fantasise about what it would be like to be in a relationship with Booth without feeling like she was crossing a line. She could imagine them coming in to work together, from the same apartment this time. She could imagine meeting him for lunch at the diner and greeting him with a kiss (he _was_ a good kisser). She could imagine him putting his arms around her at the end of a hard case and not worrying when he held on too tight or for too long because that was what he was meant to do. Because if Booth was your boyfriend, that's what he _would_ do: support you and love you with a commitment that defied anything that Brennan could possibly believe in. And that, really, was where her fantasy was proven a fantasy.

In the real world, Brennan and Booth wouldn't work like that. She could never give him what he wanted - what he needed. And she was okay with that. As long as he was happy. Well, as long as he was happy and she could still see him (she couldn't really explain that need, that _desperate_ need, so for now she skimmed over it). Given that, she was okay with their relationship as it was because he deserved more than her.

For now, it didn't matter anyway: the real world. In the Maluku islands, Brennan could be led by her dreams and her memories without hurting anyone. It wasn't as if she was changing her mind - she always came to the same conclusion - and she found that from Day 5 onwards, she was calmer than she'd been in months. And what better state was there, really, in which to make some serious anthropological breakthroughs than one of complete and utter calm, with her partner always at her shoulder.


	3. Chapter 3

**A/N: Nothing long but it's something and I'm trying to get momentum up... (Ha.) Hope you like it anyways - more soon hopefully.**

Coming home earlier than expected was disappointing, of course, but Brennan knew it was the right thing to do. And it meant, of course, that she got to see Booth. They had lunch, not by the Reflecting Pool, but in the garden of the Jeffersonian to save time for the case. Brennan breathed easier with Booth sitting next to her, she had to admit.

As he ate, she watched his profile and thought about how much she'd missed it. She would never have forgotten his face but the sheer familiarity of it rendered in front of her, in 3D HD, caused a wash of emotion to run through her. She was home. While they ate, they talked about their adventures; Booth seemed surprised when she told him about beating up the guerrillas.

"I had to. You weren't there to save me."

That was something else she'd noticed in Indonesia - how differently she acted with Booth. How she was only scared of snakes when he was there to cling to. How she was perfectly happy to beat up bad guys without his gun for protection. She found that she valued this independence (and she had to pretend Booth took some of that from her because it showed she didn't need him _like that_. That's why, when they got to talking about relationships - about his new girlfriend Hannah - she was fine with it. Really she was. She hadn't had the time or inclination to look for love (or even sex) (because she'd been thinking about Booth) so she didn't mind that she didn't have it (him).

She told him that Hannah was pretty, partly because she knew he wanted to hear it and partly just because it was true. She was at least as pretty as Brennan; it wasn't surprising that Booth was attracted to her. Brennan focused on facial symmetry, on traditional perceptions of beauty and that helped. Hannah and Booth, scientifically, seemed a good match and who was Brennan to refute science. That didn't mean that Brennan would blindly accept her though; she loved Booth, she couldn't deny it, and she would protect his feelings as much as she possibly could.


	4. Chapter 4

**A/N: Another short one, to cover some ground I think is important before things get dramatic (thanks Season 6). Hope you enjoy.**

Chapter 4

Brennan was very proud of herself. Despite some lingering feelings towards Booth which she felt it would be unhealthy to try to ignore, her priority remained his happiness. Brennan had befriended Hannah, had even given her intimate advice about Booth, and remained happy with the situation as it was. Of course, there were times when a part of her (a very small part, she assured herself) wished that she was the one going home with Booth but always, once back in her own apartment, Brennan was glad of her independence and personal space. Besides, with Booth securely involved in a romantic relationship, Brennan could reap the rewards of their partnership without worrying about the meaning of any underlying tension between them.

She wasn't sure how much Hannah knew about her and Booth's attachment to one another. Not that it really mattered, it being in the past, but Booth was always one to emphasise the value of honesty… Although, omission wasn't _technically_ its opposite.

Hannah herself was a strong woman. Everyone at the lab, including Brennan, admired her drive. Brennan could see why Booth would be drawn to someone like Hannah - independent-minded, ballsy, just a little closed off (just a little like Brennan, in other words). The story of how Booth and Hannah had met didn't really surprise Brennan either. Booth liked the dramatic and she could imagine now the look he'd given Hannah once he had her in custody: all wild admiration hidden behind a not-quite-professional, not-quite-unimpressed smirk. She tried not to think more about what Booth had been through in Afghanistan but it was hard when it was the only part of their lives for so long that they hadn't shared. And when instead of sharing them with Brennan, he had shared those experiences with Hannah.

Hannah was even getting on with Parker now. Which was good for Booth, it made him happy, but left Brennan feeling second best in the eyes of two Booth boys, instead of just one. She was still the one with the pool though, still Dr Bones, and Parker still looked at her with his big brown eyes as if she could give him the best present in the world just by talking about the job she loved. Maybe both Booths had room in their hearts for the two of them. It seemed like they did. Brennan just hoped it would stay that way.


	5. Chapter 5

**A/N:** **Set during 6x09 (The Doctor in the Photo, written by Carla Kettner) and as such the overall plot and the one line of dialogue are nothing to do with me. Hope you enjoy - Bren's emotions were kinda all over the place but I did what I could.**

Chapter 5

If it was pouring with rain like it hadn't in DC for some months (it was), Brennan didn't notice. All she could think about was finding the missing link in this case. She'd never felt such keen desperation, a desperation that had been nagging at her senses every hour of the day for the past three days. For three days, everything - Booth, Hannah, how fine they all were - had been pushed from her mind and replaced by what felt like some kind of fever. She just needed to know… To bring this woman, this talented, intelligent woman whose disappearance had been low priority to those she'd left behind, some justice.

Brennan was now across the street from the address she had scribbled down hastily and which was now being washed into the gutter by the rain. Lauren Eames had been here, Brennan knew it. There was no evidence - yet - no physical evidence to support that assertion but Brennan _knew_ , just as she imagined Booth must _know_ those times when his reasoning was inexplicable to her. Dr Eames had been here and shortly before her death. She might have even died here.

Brennan moved forwards, crossing the street but never moving her gaze from the house. Maybe she could learn something from the shadows dancing behind the thin drapes, from the neatly maintained window boxes… Something around here had to tell her _something._ Right now, she would take anything.

She saw it then, a flicker of reflective yellow out of the corner of her eye. Dr Eames' skeleton swam into Bones field of vision as she turned, leaned down and looked closer, mapping a mental path of physical evidence that led to this very spot. Was that…? Could that still be blood?

Brennan was vaguely aware that the night was getting brighter but she didn't mind; the better to see what lay before her. But the brightness began to sting her eyes and just as she looked up and realised that two tonnes of metal was coming toward her fast, a reassuringly familiar shape was pushing her out of its path: Booth was there. _Booth._

His lips were moving, asking questions that Brennan didn't register. She heard herself run off an explanation, a frantic explanation, of what she was doing here and what it all meant, all the while staring at his face and trying desperately to read his emotions in his eyes. She'd maintained not long ago that the eyes' powers to reveal inner feeling were mythic and yet, since then, she'd been made to doubt this by a virtual stranger. She wanted to doubt it again. She _needed_ to know what Booth was feeling. She needed Booth.

Somehow, he'd managed to guide her to the SUV and Brennan's mind was clearer now. Clearer now, in fact, than it had been in years. She'd spent three days in a fog, worried about her life - against all logic - and appealing to the universe for help. Well, if ever the universe were talking, nearly getting run over but being saved by the man who was there for you time and time again might just be it. Brennan didn't want to be like Lauren Eames, wasn't like her she knew now, not really but there were still some lingering similarities that she was desperate to erase. She didn't want to go with things unsaid, to die with regrets. She didn't want to be too proud, too afraid, too _whatever_ to live her life and really experience it. Some people were worth getting hurt for, Booth had shown her that, because at least you were _feeling_.

She found herself saying bits of this out loud, to Booth she supposed, explaining how Lauren Eames had never given her helicopter pilot a chance (while really appealing to Booth, asking him to forgive her for turning him down). Saying she didn't want to be like, admitting - finally - all that she'd bottled inside, that she'd thought about over and over in Maluku, that she'd pretended didn't matter now Hannah was in the picture. She wanted Booth; she wanted to try.

In the brief moment before Booth's choked reply, Brennan felt relief wash through her body. She didn't really care what happened next; she'd told Booth how she felt, against all the instincts she had built up over years of being left behind, and it felt _so good_ to speak from the heart. But then, as soon as the word "Hannah" crossed Booth's lips, reality began to set in once more forcing a weight down her throat. Honestly, in the shock and rush of the past however-many-hours-it-was, Brennan had forgotten about Hannah. Had forgotten, effectively, that Booth couldn't say yes to her, not anymore. As much as Brennan wanted him to forget Hannah, pull over the car and kiss her right then, she knew Booth couldn't and wouldn't - and she loved him a little more for it.

Brennan didn't understand how she could feel so sad, so oppressively sad, and yet so in love at the same time. So empty and yet so full of everything that was good about Booth - his smile, all his smiles, the way he looked at Parker when the three of them were sat in the diner together, they way his crisp white shirts fit around his muscled shoulders… She could've gone on. And it was this love, this fullness, that told her she didn't want Booth to lose his integrity just to say yes to her, even if her still wanted to. That wouldn't be the man she loved.

She was crying now, her eyes overflowing with months of bottled emotion. She might have been embarrassed if she had any control over her actions but, for once, she given up her self-control and let everything she had been through and felt over the past three days wash over her and fuel her sadness. What had been the point of opening her heart to him when she'd known, in her heart of hearts, what he'd say? If she'd been thinking straight… Well, the point was she _had_ been. She had thought clearly about what she wanted, only too late. She had missed her chance.

Some part of Brennan felt Booth's eyes on her and fought her self-pity to remove that God-awful look from his face. She couldn't bear Booth's reaction to causing her pain and yet hiding the extent of it when sleep-deprived was nigh on impossible. Still, it wasn't fair on him to fall apart like this. She wasn't his responsibility, not really, not outside of work hours. So, Brennan pulled herself up in her seat, willed the lump in her throat away and forced herself to look towards her partner.

"It's okay," she told him, trying hard to believe it herself. "My whole world turned upside down. I can adjust."

And she could readjust, sure, to the world she had left behind three days ago but from now on, Brennan was going to be a changed person living in it.


	6. Chapter 6

**A/N:** **So here's this, set at the end of 'The Daredevil in the Mold' by Dean Lopata (all dialogue's his). Hope you like it - any feedback always welcome.**

Chapter 6

Brennan didn't really think once Hannah was done talking. She barely even had the voice to reply (though she thought managed something about 'sorry' and 'I understand'). For once, Brennan acted on instinct, ended the conversation as soon as she could and headed out the door. Hannah hadn't been sure where Booth was headed, only that he'd left the apartment free for her to collect her stuff, but Brennan had a pretty good idea where he might be.

She could see him before she entered, nursing a whiskey and at least three empty shot glasses. _Booth._ Brennan pushed through the door, walking carefully over to the bar. She'd never seen Booth like this - so without hope. He was always the one reminding her to look on the bright side, to trust to the universe. As she sat down, she said the only thing she could think to say: "You drunk?"

His words were slurred - he was drunk - but he was still bickering with her, playing with her words. It didn't take him long to notice that something was up though - after all he could read people as well as she could read bones - and when he asked, Brennan told him the truth: that Hannah had called her. And then she wished she hadn't; his face darkened and he turned away, shutting her out.

"Just, I really, I-I don't want to talk about that. Okay? I'm just over- I'm over it. I'm done okay?"

Hannah had spilled out most of what had happened on the phone - Brennan had become her closest friend in DC, after all - but Brennan wanted to hear it from Booth. She wanted Booth to tell her that this was a rough patch, sure, but he was going to be ok.

"So what happens next?"

He turned back to her when she spoke, swirling his whiskey around his glass, his eyes stormy.

"What happens next? What I mean, you like evidence, right, Bones? Well, here's the evidence.

The evidence is that there's something wrong here. Now, I-I fell in love with a woman. I had a kid.

She doesn't want to marry me. Well, and... And then the next woman, well, she's..."

"Me."

She was one of the reasons Booth was in this state. It hurt that she'd hurt him but she could hardly deny it. Not when she was now feeling for herself what she imagined she'd put Booth through.

"Yeah," he nodded towards her. "And now I mean, what is it with women who just don't want what I'm offering here?"

"Booth." Don't talk like that. Don't be stupid. Women want what you're offering. Brennan thought all this and said none of it because Booth did have a point. Time after time, Booth, one of the most committed, good guys Brennan had ever known was turned down. He sure knew you how to pick exactly the women who would struggle with the concept of unconditional, everlasting love.

"No. Just...You know what? Drink. Drink. I'm just really- I'm just mad. I'm just really mad at all of you. I am just mad."

He seemed like he was losing it now but Brennan couldn't think of anything to do. It was hard to take Booth's anger personally even when, rationally, she knew that 1) he was drunk and 2) it was Hannah who had most recently rejected him. Still, this felt like a speech Booth had been working on for a while and, while she hadn't rejected him _most recently_ , she had rejected him. Even when he'd offered her everything she thought she could never have. Booth seemed to have calmed down a little though. He even seemed determined.

"Okay, so, you wanna know how this is gonna work?"

Brennan said nothing and waited for him to continue.

" Okay, this is how this is gonna work. Me and you are partners. That's what we do. We're partners. All right? And I love that."

She loved that too. More than she'd ever expected she would and more than she ever really cared to admit. Booth was her partner, her rock and her constant through whatever was thrown at them. She loved that too.

"I think that's great," Booth continued. "And, uh, we're-we're good people who catch bad people. Right? Yeah. And-And And we argue. We go back and forth. We're partners. And sometimes after we solve a case we come here and we celebrate. That's what we do. We celebrate. So as far as I can see that is what happens next."

Brennan was a little confused. From what she could tell of Booth's drunken ramblings, he was saying that what came next was them celebrating and Brennan just couldn't make it the cause.

"Are you okay with that?" He was looking straight at her again, his eyes almost harsh, challenging her to something. "Great, because, you know, if you are, I'll tell you what. You stay here and you have a drink with me. All right? Maybe, uh we have a little small talk, chitchat. And if you're not, well you can leave. There's the door. And, uh, tomorrow I'll find you a new F.B.I. guy."

Brennan paused within herself. There was no way in hell she was ever going to work with another FBI agent. No way on this Earth. But what Booth seemed to be saying, if she was reading this right - and she wasn't always that good with inference - was that they were going to partners for the foreseeable future. Just partners. Except, to Brennan, there was really no _just_ about it. Even after she'd rejected Booth romantically, she'd clung to their partnership. If only she'd seen the signs then... But she hadn't so it didn't matter now. He'd agreed to continue then.

"Those are my only choices?" She needed to clarify, just in case.

"Yeah. Those are your only choices." He may as well have said "That's your only choice" for all Brennan was dithering.

"Then I'll have a drink."

And she did.


	7. Chapter 7

**A/N: I'm sorry it's been awhile and that this is a bit short. Thank you for reading - all your feedback has been much appreciated.**

 **Set at the end of 'The Bikini in the Soup' by Lyla Oliver (dialogue's hers) - hope you enjoy.**

Chapter 7

Brennan wasn't sure exactly when she'd decided that she was going to spend this Valentine's Day with Booth. In fact, she was pretty sure that that decision hadn't been conscious. She just knew that, instead of finding herself walking out of the Jeffersonian to begin the frosty February walk back to her apartment, she'd ended up even deeper within the museum, inspecting the 1920s exhibit. Even then, she still thought she'd be spending the evening alone; she just wanted to think about Booth a little bit, to smile at the fact that, in his current state, the only thing he could associate happily with Valentine's Day was the Massacre.

Brennan wondered slowly around the exhibit; she had nowhere to be, no date who would miss her. She couldn't remember the last time she'd stayed late at work just to admire the building. When she'd first started, this had been a regular occurrence - before she'd met Angela, before she'd realised that maybe Jack Hodgins wasn't so bad, before she'd employed Zack... Before Booth. Now, Brennan had things to do after work: write, drink at the Founding Fathers, visit friends or have them round - and she had to admit that she liked that just as much as the exhibits, maybe even more. Definitely even more. Besides, the people in this exhibit especially hadn't gained their place in it by living their lives inside museums. Opening hours were long over so Brennan didn't have to worry about craning her neck over the crowds in front of her to read the information in each case. She could meander as aimlessly as she wanted across each room without getting in anyone's way. She could pause suddenly in front of the gun exhibit, without knowing when or why she'd decided to... And once she had done, she had full freedom to follow up on an irrepressible urge to call in a favour.

She stuck her head through the door ahead of her body, hands clutching the wheeled table tightly. Gunfire reverberated rhythmically around the room. Bang, click pause bang, click pause - bang. Brennan progressed further into the room, prompting Booth to turn to see who was approaching. His face creased into a look of surprise.

"Bones, what are you doing here?"

Brennan grinned cheekily back at him. She loved that she could still catch him off guard and, she had to admit to herself even if to no-one else, she loved the way he called her 'Bones'. Not _that_ he did but the way he did - softly and rounded, admonishing yet (maybe, just maybe) happy to see her. Looking back, she'd realise that that was when she'd decided to spend that Valentine's Day with Booth - as well as as many after that as she possibly could.


End file.
